Generating high quality reference genomes from field collected specimens by optimizing preservation

Minich, Jeremiah J.; Moore, Malia L.; Allsing, Nicholas A; Murray, Emily R; Tran, Loi; Michael, Todd P.

doi:10.1101/2023.03.10.532097

Cited by 1 publication

(1 citation statement)

References 23 publications

(20 reference statements)

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“…After being adequately charged with LN2, dry vapor shippers can keep samples ultra-cold for a week or more in the field. While LN2 is the gold standard, other preservatives like 95% EtOH, 20-25% DMSO in EDTA may adequately preserve DNA for long-read sequencing, although efficacy may vary depending on the tissue type [167, 173]. Other options include lysis buffers or commercial products such as Zymo DNA/RNA shield (Zymo Research, USA).…”

Section: Advancing Research and Conservation Through Amphibian Genomicsmentioning

confidence: 99%

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Kosch,

Torres-Sánchez,

Liedtke

et al. 2024

Preprint

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Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomics resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti- predator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and outline how the AGC can enable amphibian genomics research to “leap” to the next level.

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Section: Advancing Research and Conservation Through Amphibian Genomicsmentioning

confidence: 99%

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Kosch,

Torres-Sánchez,

Liedtke

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

Generating high quality reference genomes from field collected specimens by optimizing preservation

Cited by 1 publication

References 23 publications

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

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